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Re: Had "they do" in the below sentence better be omitted?

Omissibility is one of the characteristics of English and other languages. But it can't be used arbitrarily, because it may result in syntactic ambiguity.
One can say that omitting it will not hurt the message and the preposition can clarify the relation; we shouldn't ignore the concept of expectancy chain though.

Re: Had "they do" in the below sentence better be omitted?

The X interactions play a more important role in system A than they do in system B.

Please help me correct the sentence if it's not grammatical.

Thanks.

I think, you need the expression, because, here ‘than’ acts as a conjunction to introduce a subordinate clause(they do in system B). Let us consider a similar example, you say: They spend more time in extracurricular activities than they do in study. (not than in study)

Re: Had "they do" in the below sentence better be omitted?

Yes, I agree that it's more faithful to English formal structure to preserve it, but the fact that it's functioning as a conjunction isn't the best reason.
Take a look at this:
I like playing football and basketball.

And is connecting a complete sentence to an implied one.

It's an acceptable structure, but from a semantic perspective, and as I've already mentioned, the sentence suffers from ambiguity:
1. I like playing football andI like playing basketball.
2. I like playing football and I like basketball[but I don't like playing basketball].

But the following one is overtly wrong without any further thinking, because it compares two heterogeneous entities:
-The paintings in this gallery are similar to that gallery.
So it's a matter of syntax and semantics. Sometimes it works and sometimes it doesn't, depending on the sentence.

Now, apart from grammar and things of that sort, I'm willing to know if you're interested in morphology and etymology. Indian was a very influential language in the formation of many words and concepts. We can talk about such issues from time to time. What do you think?